static mitk::Image::Pointer TransformToReference(mitk::Image *reference, mitk::Image *moving, bool sincInterpol = false)
{
// Convert to itk Images
InputImageType::Pointer itkReference = InputImageType::New();
InputImageType::Pointer itkMoving = InputImageType::New();
mitk::CastToItkImage(reference,itkReference);
mitk::CastToItkImage(moving,itkMoving);
// Identify Transform
typedef itk::IdentityTransform<double, 3> T_Transform;
T_Transform::Pointer _pTransform = T_Transform::New();
_pTransform->SetIdentity();
typedef itk::WindowedSincInterpolateImageFunction< InputImageType, 3> WindowedSincInterpolatorType;
WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
typedef itk::ResampleImageFilter<InputImageType, InputImageType> ResampleFilterType;
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInput(itkMoving);
resampler->SetReferenceImage( itkReference );
resampler->UseReferenceImageOn();
resampler->SetTransform(_pTransform);
resampler->SetInterpolator(sinc_interpolator);
resampler->Update();
// Convert back to mitk
mitk::Image::Pointer result = mitk::Image::New();
result->InitializeByItk(resampler->GetOutput());
GrabItkImageMemory( resampler->GetOutput() , result );
return result;
}
FilterImageType::Pointer gaussTransform(const FilterImageType::Pointer sourceImage, FilterImageType::SizeType destSize,
float gaussSigma, const BaseTransformType *transform) {
std::cerr << "Filter, Transformation and Output start" << std::endl;
itk::TimeProbesCollectorBase collector;
collector.Start( "Filter, Transformation and Output" );
collector.Start( "Filter" );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::SizeType sourceSize = sourceImage->GetBufferedRegion().GetSize();
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::ConstPointer temp;
#ifdef useFastMemoryHungryGaussian
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 0 ); // 0 --> X direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( sourceImage );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 1 ); // 1 --> Y direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetDirection( 2 ); // 2 --> Z direction
filter->SetOrder( GaussFilterType::ZeroOrder );
filter->SetSigma( gaussSigma );
filter->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
#else
{
GaussFilterType::Pointer filter = GaussFilterType::New();
filter->SetUseImageSpacingOn();
filter->SetVariance( std::sqrt(gaussSigma) );
filter->SetInput( sourceImage );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
try { filter->Update(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
temp = filter->GetOutput();
}
#endif
collector.Stop( "Filter" );
InterpolatorType::Pointer interpolator = InterpolatorType::New();
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInterpolator( interpolator );
IdentityTransformType::Pointer identPointer;
if (transform == NULL) {
identPointer = IdentityTransformType::New();
transform = identPointer;
}
resampler->SetTransform( transform );
FilterImageType::SpacingType destSpacing;
for(unsigned int i = 0; i < Dimension; ++i) {
destSpacing[i] = sourceImage->GetSpacing()[i] * float(sourceSize[i]) / float(destSize[i]);
}
resampler->SetInput( temp );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
resampler->SetSize( destSize );
resampler->SetOutputSpacing( destSpacing );
resampler->SetOutputOrigin( sourceImage->GetOrigin() );
resampler->SetDefaultPixelValue( 0 );
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
FilterImageType::Pointer result;
try { resampler->Update(); result = resampler->GetOutput(); }
catch( itk::ExceptionObject & excep ) { std::cerr << "Exception caught !" << std::endl << excep << std::endl; }
std::cerr << "dbg:" << __FILE__ << " line:" << __LINE__ << std::endl;
collector.Stop( "Filter, Transformation and Output" );
collector.Report();
std::cerr << "Filter, Transformation and Output end" << std::endl;
return result;
}
void mitk::RegistrationWrapper::ApplyTransformationToImage(mitk::Image::Pointer img, const mitk::RegistrationWrapper::RidgidTransformType &transformation,double* offset, mitk::Image* resampleReference, bool binary)
{
typedef mitk::DiffusionImage<short> DiffusionImageType;
if (dynamic_cast<DiffusionImageType*> (img.GetPointer()) == NULL)
{
ItkImageType::Pointer itkImage = ItkImageType::New();
MITK_ERROR << "imgCopy 0 " << "/" << img->GetReferenceCount();
MITK_ERROR << "pixel type " << img->GetPixelType().GetComponentTypeAsString();
CastToItkImage(img, itkImage);
typedef itk::Euler3DTransform< double > RigidTransformType;
RigidTransformType::Pointer rtransform = RigidTransformType::New();
RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
for (int i = 0; i<6;++i)
parameters[i] = transformation[i];
rtransform->SetParameters( parameters );
mitk::Point3D origin = itkImage->GetOrigin();
origin[0]-=offset[0];
origin[1]-=offset[1];
origin[2]-=offset[2];
mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(origin);
itk::Matrix<double,3,3> dir = itkImage->GetDirection();
itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
itk::Matrix<double,3,3> newDirection = transM * dir;
itkImage->SetOrigin(newOrigin);
itkImage->SetDirection(newDirection);
// Perform Resampling if reference image is provided
if (resampleReference != NULL)
{
typedef itk::ResampleImageFilter<ItkImageType, ItkImageType> ResampleFilterType;
ItkImageType::Pointer itkReference = ItkImageType::New();
CastToItkImage(resampleReference,itkReference);
typedef itk::WindowedSincInterpolateImageFunction< ItkImageType, 3> WindowedSincInterpolatorType;
WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New();
typedef itk::NearestNeighborInterpolateImageFunction< ItkImageType, double > NearestNeighborInterpolatorType;
NearestNeighborInterpolatorType::Pointer nn_interpolator = NearestNeighborInterpolatorType::New();
ResampleFilterType::Pointer resampler = ResampleFilterType::New();
resampler->SetInput(itkImage);
resampler->SetReferenceImage( itkReference );
resampler->UseReferenceImageOn();
if (binary)
resampler->SetInterpolator(nn_interpolator);
else
resampler->SetInterpolator(sinc_interpolator);
resampler->Update();
GrabItkImageMemory(resampler->GetOutput(), img);
}
else
{
// !! CastToItk behaves very differently depending on the original data type
// if the target type is the same as the original, only a pointer to the data is set
// and an additional GrabItkImageMemory will cause a segfault when the image is destroyed
// GrabItkImageMemory - is not necessary in this case since we worked on the original data
// See Bug 17538.
if (img->GetPixelType().GetComponentTypeAsString() != "double")
img = GrabItkImageMemory(itkImage);
}
}
else
{
DiffusionImageType::Pointer diffImages = dynamic_cast<DiffusionImageType*>(img.GetPointer());
typedef itk::Euler3DTransform< double > RigidTransformType;
RigidTransformType::Pointer rtransform = RigidTransformType::New();
RigidTransformType::ParametersType parameters(RigidTransformType::ParametersDimension);
for (int i = 0; i<6;++i)
{
parameters[i] = transformation[i];
}
rtransform->SetParameters( parameters );
mitk::Point3D b0origin = diffImages->GetVectorImage()->GetOrigin();
b0origin[0]-=offset[0];
b0origin[1]-=offset[1];
b0origin[2]-=offset[2];
mitk::Point3D newOrigin = rtransform->GetInverseTransform()->TransformPoint(b0origin);
itk::Matrix<double,3,3> dir = diffImages->GetVectorImage()->GetDirection();
itk::Matrix<double,3,3> transM ( vnl_inverse(rtransform->GetMatrix().GetVnlMatrix()));
itk::Matrix<double,3,3> newDirection = transM * dir;
diffImages->GetVectorImage()->SetOrigin(newOrigin);
diffImages->GetVectorImage()->SetDirection(newDirection);
diffImages->Modified();
mitk::DiffusionImageCorrectionFilter<short>::Pointer correctionFilter = mitk::DiffusionImageCorrectionFilter<short>::New();
// For Diff. Images: Need to rotate the gradients (works in-place)
correctionFilter->SetImage(diffImages);
correctionFilter->CorrectDirections(transM.GetVnlMatrix());
img = diffImages;
}
}
